Studies involving minimalist shoes have dramatically increased this past 10 years. While a deeper knowledge of the related modifications has ensued regarding the kinematics, electromyographic, and dynamic patterns, little is known regarding the modifications at the muscle forces and muscle fiber levels. The aim of the present study was to assess at a muscular level the modifications brought up when running barefoot using 0 mm midsole height running shoe, or using classical midsole height running shoes. An EMG-Driven model that combines the kinematics, dynamics, and electromyographic data was used to estimate the Triceps Surae (TS) muscle forces and fiber behavior during running using different footwear conditions. Despite differences at the joint level between barefoot and shod running when looking at ankle joint range of motion, or foot-ground angle at touchdown, the results showed no effect of footwear neither on the maximal muscle forces nor on the relative amount of force produced by each muscle within the TS muscle group when wearing different footwear. On the contrary, different behaviors of muscle fibers were shown with lower amplitudes of fiber lengths for the Gastrocnemii biarticular muscles when running barefoot. This particular results reveal that wearing a shoe, even with a very thin sole, could deeply modify the intricate muscle-tendon mechanics of running.